A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record

Proceedings of the Royal Society B: Biological Sciences

Volumn 273, Issue 1596, 2006, Pages 1867-1872

  Berney, Cédric ^a,b   Pawlowski, Jan ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Molecular dating; Origin of eukaryotes; Protist phylogeny; Relaxed molecular clock; Small subunit ribosomal RNA gene

Indexed keywords

SMALL SUBUNIT RIBOSOMAL RNA; RIBOSOME RNA;

DIATOM; DINOFLAGELLATE; EUKARYOTE; EVOLUTION; FOSSIL RECORD; MICROFOSSIL; MOLECULAR ANALYSIS; ORIGIN OF LIFE; PROTEROZOIC; RNA; TIMESCALE;

ARTICLE; CONTROLLED STUDY; DIATOM; DINOFLAGELLATE; EUKARYOTE EVOLUTION; MESOPROTEROZOIC; MICROFOSSIL; MOLECULAR CLOCK; NEOPROTEROZOIC; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; AMOEBA; ANIMAL; CLASSIFICATION; EUKARYOTIC CELL; FOSSIL; FUNGUS; GENETICS; GREEN ALGA; MOLECULAR EVOLUTION; RED ALGA;

BACILLARIOPHYTA; DINOPHYCEAE; EUKARYOTA; HAPTOPHYCEAE; PROTISTA;

ALGAE, GREEN; ALGAE, RED; AMOEBA; ANIMALS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FOSSILS; FUNGI; PHYLOGENY; RNA, RIBOSOMAL;

EID: 33750618212     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2006.3537     Document Type: Article

References (41)

1. Aris-Brosou, S. & Yang, Z. 2003 Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa. Mol. Biol. Evol. 20, 1947-1954. (doi:10.1093/molbev/msg226)
2. Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. 2000 A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977. (doi:10.1126/science.290.5493.972)
3. Benton, M. J. & Ayala, F. J. 2003 Dating the tree of life. Science 300, 1698-1700. (doi:10.1126/science.1077795)
4. Blair, J. E. & Hedges, S. B. 2005 Molecular clocks do not support the Cambrian explosion. Mol. Biol. Evol. 22, 387-390. (doi:10.1093/molbev/msi039)
5. Brasier, M. D., Green, O. R., Jephcoat, A. P., Kleppe, A. K., Van Kranendonk, M. J., Lindsay, J. F., Steele, A. & Grassineau, N. V. 2002 Questioning the evidence for Earth's oldest fossils. Nature 416, 76-81. (doi:10.1038/416076a)
6. Brocks, J. J., Logan, G. A., Buick, R. & Summons, R. E. 1999 Archean molecular fossils and the early rise of eukaryotes. Science 285, 1033-1036. (doi:10.1126/science.285.5430.1033)
7. Butterfield, N. J. 2000 Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386-404.
8. Butterfield, N. J. 2004 A vaucheriacean alga from the middle Neoproterozoic of Spitsbergen: implications for the evolution of Proterozoic eukaryotes and the Cambrian explosion. Paleobiology 30, 231-252.
9. Butterfield, N. J. 2005 Probable Proterozoic fungi. Paleobiology 31, 165-182.
10. Butterfield, N. J., Knoll, A. H. & Swett, K. 1994 Paleobiology of the Neoproterozoic Svanbergfjellet Formation, Spitsbergen. Fossil Strata 34, 1-84.
11. Cavalier-Smith, T. 2002a The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int. J. Syst. Evol. Microbiol. 52, 7-76.
12. Cavalier-Smith, T. 2002b The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52, 297-354.
13. Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F. & Philippe, H. 2004 The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc. Natl Acad. Aci. USA 101, 15 386-15 391. (doi:10.1073/pnas.0403984101)
14. Falkowski, P. G., Katz, M. E., Knoll, A. H., Quigg, A., Raven, J. A., Schofield, O. & Taylor, F. J. R. 2004 The evolution of modern eukaryotic phytoplankton. Science 305, 354-360. (doi:10.1126/science.1095964)
15. Graur, D. & Martin, W. 2004 Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet. 20, 80-86. (doi:10.1016/j.tig.2003.12.003)
16. Guindon, S. & Gascuel, O. 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704. (doi:10.1080/10635150390235520)
17. Hedges, S. B. & Kumar, S. 2004 Precision of molecular time estimates. Trends Genet. 20, 242-247. (doi:10.1016/j.tig.2004.03.004)
18. Hedges, S. B., Chen, H., Kumar, S., Wang, D. Y., Thompson, A. S. & Watanabe, H. 2001 A genomic timescale for the origin of eukaryotes. BMC Evol. Biol. 1, 4. (doi:10.1186/1471-2148-1-4)
19. Hedges, S. B., Blair, J. E., Venturi, M. L. & Shoe, J. L. 2004 A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol. 4, 2. (doi:10.1186/1471-2148-4-2)
20. Hoffman, P. H. 1987 Early Proterozoic foredeeps, foredeep magmatism, and superior-type iron-formations of the Canadian Shield. In Proterozoic lithospheric evolution (ed. A. Kröner), pp. 85-98. Washington, DC: American Geophysical Union.
21. Huelsenbeck, J. P. & Ronquist, F. 2001 MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (doi:10.1093/bioinformatics/17.8.754)
22. Kishino, H., Thorne, J. L. & Bruno, W. J. 2001 Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352-361.
23. Knoll, A. H. 1994 Proterozoic and early Cambrian protists: evidence for accelerating evolutionary tempo. Proc. Natl Acad. Sci. USA 91, 6743-6750.
24. Larsen, N., Olsen, G. J., Maidak, B. L., McCaughey, M. J., Overbeek, R., Macke, T. J., Marsh, T. L. & Woese, C. R. 1993 The ribosomal database project. Nucleic Acids Res. 21, 3021-3023.
25. Lee, M. S. 1999 Molecular clock calibrations and metazoan divergence dates. J. Mol. Evol. 49, 385-391. (doi:10.1007/PL00006562)
26. Loeblich, A. R. & Tappan, H. 1964 Sarcodina - chiefly 'Thecamoebians' and Foraminiferida. In Treatise on invertebrate paleontology, Part C, Protista 2 (ed. R. C. Moore), pp. 1-900. Lawrence, KS: University of Kansas Press.
27. Moorbath, S. 2005 Palaeobiology: dating earliest life. Nature 434, 155. (doi:10.1038/434155a)
28. Nikolaev, S. I., Berney, C., Fahrni, J. F., Bolivar, I., Polet, S., Mylnikov, A. P., Aleshin, V. V., Petrov, N. B. & Pawlowski, J. 2004 The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc. Natl Acad. Sci. USA 101, 8066-8071. (doi:10.1073/pnas.0308602101)
29. Philippe, H. & Adoutte, A. 1998 The molecular phylogeny of Protozoa: solid facts and uncertainties. In Evolutionary relationships among Protozoa (ed. G. H. Combs, K. Vickerman, M. A. Sleigh & A. Warren), pp. 25-56. London, UK: Chapman & Hall.
30. Porter, S. M. & Knoll, A. H. 2000 Testate amoebae in the Neoproterozoic era: evidence from vase-shaped microfossils in the Chuar Group, Grand Canyon. Paleobiology 26, 360-385.
31. Reisz, R. R. & Müller, J. 2004 Molecular timescales and the fossil record: a paleontological perspective. Trends Genet. 20, 237-241. (doi:10.1016/j.tig.2004.03.007)
32. Rodriguez, F., Oliver, J. L., Marin, A. & Medina, J. R. 1990 The general stochastic model of nucleotide substitution. J. Theor. Biol. 142, 485-501.
33. Smirnov, A., Nassonova, E., Berney, C., Fahrni, J., Bolivar, I. & Pawlowski, J. 2005 Molecular phylogeny and classification of the lobose amoebae. Protist 156, 129-142. (doi:10.1016/j.protis.2005.06.002)
34. Stechmann, A. & Cavalier-Smith, T. 2003 The root of the eukaryote tree pinpointed. Curr. Biol. 13, R665-R666. (doi:10.1016/S0960- 9822(03)00602-X)
35. van Zuilen, M. A., Lepland, A. & Arrhenius, G. 2002 Reassessing the evidence for the earliest traces of life. Nature 418, 627-630. (doi:10.1038/nature00934)
36. Wang, D. Y., Kumar, S. & Hedges, S. B. 1999 Divergence time estimates for the early history of animal phyla and the origin of plants, animals, and fungi. Proc. R. Soc. B 266, 163-171. (doi:10.1098/rspb.1999.0617)
37. Welch, J. J. & Bromham, L. 2005 Molecular dating when rates vary. Trends Ecol. Evol. 20, 320-327. (doi:10.1016/j.tree.2005.02.007)
38. Woods, K. N., Knoll, A. H. & German, T. 1998 Xanthophyte algae from the Mesoproterozoic/Neoproterozoic transition: confirmation and evolutionary implications. Geol. Soc. Am. Abstr. Program 30, 232.
39. Wuyts, J., De Rijk, P., Van de Peer, Y., Pison, G., Rousseeuw, P. & De Wachter, R. 2000 Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res. 28, 4698-4708. (doi:10.1093/nar/28.23. 4698)
40. Yang, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
41. Zhang, Z. 1986 Clastic facies microfossils from the Chuanlinggou Formation (1800 Ma) near Jixian, North China. J. Micropaleontol. 5, 9-16.